Markdown Syntax

The body of the document is where you will do your writing. Writing will happen primarily in the Markdown format (LaTeX and HTML would also work, depending on the output format).

Markdown is a lightweight markup language that you can use to add formatting elements to plaintext text documents. - Markdown Guide

Learning Markdown

If you’re not familiar with Markdown, you can familiarize yourself with it in a couple of minutes using the following link: https://www.markdownguide.org/cheat-sheet/.

You can also use the Visual Editor in VS Code or RStudio, to see Markdown syntax previewed in it’s final format as you write. The Visual Editor also has some common Word-like shortcuts, such as Ctrl + B to make text bold.

Markdown Sneak Peek: Text Formatting

*italics* and **bold**

superscript^2^ / subscript~2~

~~strikethrough~~

`verbatim code`

Markdown Sneak Peek: Tables

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|   12  |  12  |    12   |    12  |
|  123  |  123 |   123   |   123  |
|    1  |    1 |     1   |     1  |

Exercise

1. Go to the Markdown Syntax chapter in the workshop book and refer to the text provided in the Exercise section.

2. Copy the text into your Quarto document, like an Introduction of sorts, and reformat it with Markdown Syntax

3. Render the document to HTML.

BibText Keys

Now that we know how to write in Markdown and run analyses in code chunks, let’s learn about referencing using BibTex keys!

A typical BibTex key might look like the following:

@article{nash51,
  author  = "Nash, John",
  title   = "Non-cooperative Games",
  journal = "Annals of Mathematics",
  year    = 1951,
  volume  = "54",
  number  = "2",
  pages   = "286--295"
}

Working With BibTex Keys

We will work with with bibliographies in the form of .bib files. .bib stands for BibTeX Bibliographical Database. They are text files which contain a list of references in the form of BibTex keys.

Here is an example of another BibTex key for a reference used in this workshop:

@misc{RMarkdownWritingReproducible,
    title = {{RMarkdown} for writing reproducible scientific papers},
    url = {https://libscie.github.io/rmarkdown-workshop/handout.html},
    urldate = {2023-04-18},
    file = {RMarkdown for writing reproducible scientific papers:C\:\\Users\\Moope001\\Zotero\\storage\\SJITSZZI\\handout.html:text/html},
}

Working with BibTex keys

In practice, your .bib file should be updated along the way to include the BibTex keys for all your references. You can cite a specific reference using the the @ character with the key/identifier in the first line of the entry.

For the previously mentioned examples, it would be:

• In-Text Citations: @nash51 OR @RMarkdownWritingReproducible

• Bracketed Citations: [@nash51] OR [@nash51, @RMarkdownWritingReproducible]

More information can be found at: https://quarto.org/docs/authoring/footnotes-and-citations.html

Exercise

Go to the Referencing chapter in the workshop book and refer to the instructions in the Exercise section.

You will go through the workflow of creating a .bib file that will be automatically updated by Zotero and integrating it with your Quarto document.